Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H

Computation of free energy differences through nonequilibrium stochastic dynamics: The reaction coordinate case

3 D quantum scattering calculations of the reaction He + H , + +

An improved version of the S-matrix Kohn variational method has been applied to calculating 3D quantum reaction probabilities of the ion-molecular reaction He+ HT (u) AHeH+ + H. The calculation is carried out for total angular momentum J= 0 and employs the DIM potential surface of Kuntz. Our results show that vibrational excitation of H: enhances the reaction probabilities and are in qualitativ...

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the re...

Two-dimensional reaction free energy surfaces of catalytic reaction: effects of protein conformational dynamics on enzyme catalysis.

We introduce a two-dimensional (2D) multisurface reaction free energy description of the catalytic cycle that explicitly connects the recently observed multi-time-scale conformational dynamics as well as dispersed enzymatic kinetics to the classical Michaelis-Menten equation. A slow conformational motion on a collective enzyme coordinate Q facilitates the catalytic reaction along the intrinsic ...

comparison of catalytic activity of heteropoly compounds in the synthesis of bis(indolyl)alkanes.

heteropoly acids (hpa) and their salts have advantages as catalysts which make them both economically and environmentally attractive, strong br?nsted acidity, exhibiting fast reversible multi-electron redox transformations under rather mild conditions, very high solubility in polar solvents, fairly high thermal stability in the solid states, and efficient oxidizing ability, so that they are imp...